So, I programmed an ATMEGA32u4 and when I connect the device, it doesn't run the code. Instead, it gets recognised as an ATMEGA32u4 chip in Windows device manager.
To get the code running I have to open Atmel FLIP and open USB and then have to press the start application button after which it gets recognised as a HID in device manager and works as intended. I don't know why and what is happening.
The reset is pulled high with a 10k and the HWB is pulled down with a 10k and the chip has the factory bootloader on it.(if this helps)